Read data

source(paste0(root.dir, 'scripts/myRLib.R'))
funcset <- readLines(paste0(root.dir, 'output-run_step2/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/sig_subset.set'))
funcset <- parseFuncSet(funcset)
funcset.names <- names(funcset)
xtyi.files <- strsplit('output-direction_XT_YI/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p1.0000e+00.assoc.logistic:output-direction_XT_YI/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p3.0000e-01.assoc.logistic:output-direction_XT_YI/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p1.0000e-01.assoc.logistic:output-direction_XT_YI/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p3.0000e-02.assoc.logistic:output-direction_XT_YI/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p1.0000e-02.assoc.logistic:output-direction_XT_YI/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p3.0000e-03.assoc.logistic:output-direction_XT_YI/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p1.0000e-03.assoc.logistic:output-direction_XT_YI/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p3.0000e-04.assoc.logistic:output-direction_XT_YI/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/xtyi_LDpred_p1.0000e-04.assoc.logistic', ':')[[1]]
ps <- strsplit('1,0.3,0.1,0.03,0.01,0.003,0.001,0.0003,0.0001', ',')[[1]]
inter.files <- strsplit('output-run_step2/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p1.0000e+00.assoc.logistic:output-run_step2/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p3.0000e-01.assoc.logistic:output-run_step2/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p1.0000e-01.assoc.logistic:output-run_step2/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p3.0000e-02.assoc.logistic:output-run_step2/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p1.0000e-02.assoc.logistic:output-run_step2/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p3.0000e-03.assoc.logistic:output-run_step2/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p1.0000e-03.assoc.logistic:output-run_step2/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p3.0000e-04.assoc.logistic:output-run_step2/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/interaction.sig_subset_LDpred_p1.0000e-04.assoc.logistic', ':')[[1]]
prs.files <- strsplit('../step1/output-run_step1/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p1.0000e+00.txt:../step1/output-run_step1/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p3.0000e-01.txt:../step1/output-run_step1/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p1.0000e-01.txt:../step1/output-run_step1/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p3.0000e-02.txt:../step1/output-run_step1/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p1.0000e-02.txt:../step1/output-run_step1/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p3.0000e-03.txt:../step1/output-run_step1/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p1.0000e-03.txt:../step1/output-run_step1/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p3.0000e-04.txt:../step1/output-run_step1/MAGNETIC_LDL.C__wtccc_cad__wtccc_ctrl/ldpred_LDpred_p1.0000e-04.txt', ':')[[1]]

Epistasis

for (i in 1:length(xtyi.files)) {
    cat("##", funcset.names[i])
    cat("
")
    cat("
")
    snp.subset <- funcset[[funcset.names[i]]]
    
    # read I ~ SNP
    prs <- read.table(paste0(root.dir, prs.files[i]), header = T)
    prs$sid <- as.character(prs$sid)
    prs.sub <- prs[prs$sid %in% snp.subset, ]
    
    # read others
    xtyi <- read.table(paste0(root.dir, xtyi.files[i]), header = T)
    xtyi$SNP <- as.character(xtyi$SNP)
    yt.xtyi <- xtyi[(xtyi$SNP %in% snp.subset) & (xtyi$SNP %in% 
        prs.sub$sid), ]
    yt.xtyi.xt <- yt.xtyi[yt.xtyi$TEST == "ADD", ]
    yt.xtyi.yi <- yt.xtyi[yt.xtyi$TEST == "PRS", ]
    inter <- read.table(paste0(root.dir, inter.files[i]), header = T)
    inter$SNP <- as.character(inter$SNP)
    inter <- inter[inter$TEST == "ADDxPRS", ]
    yt.inter <- inter[(inter$SNP %in% snp.subset) & (inter$SNP %in% 
        prs.sub$sid), ]
    
    # order all rows
    yt.xtyi.xt <- yt.xtyi.xt[order(yt.xtyi.xt$SNP), ]
    yt.xtyi.yi <- yt.xtyi.yi[order(yt.xtyi.yi$SNP), ]
    yt.inter <- yt.inter[order(yt.inter$SNP), ]
    prs.sub <- prs.sub[order(prs.sub$sid), ]
    
    # check direction
    prs.sub$nt1 <- as.character(prs.sub$nt1)
    yt.xtyi.xt$A1 <- as.character(yt.xtyi.xt$A1)
    yt.inter$A1 <- as.character(yt.inter$A1)
    if (sum(prs.sub$nt1 != yt.xtyi.xt$A1) != 0 | sum(prs.sub$nt1 != 
        yt.inter$A1) != 0) {
        print("Direction does not match. Exit!")
        quit()
    }
    
    yt.xtyi.xt.mean.std <- getMeanStd(yt.xtyi.xt$SNP, yt.xtyi.xt$P, 
        yt.xtyi.xt$OR, "Y~Gi+I (Gi)")
    yt.xtyi.yi.mean.std <- getMeanStd(yt.xtyi.yi$SNP, yt.xtyi.yi$P, 
        yt.xtyi.yi$OR, "Y~Gi+I (I)")
    yt.inter.mean.std <- getMeanStd(yt.inter$SNP, yt.inter$P, 
        yt.inter$OR, "Y~Gi*I")
    prs.sub.mean.std <- data.frame(SNP = prs.sub$sid, Mean = prs.sub$ldpred_beta, 
        Std = 0, Type = "I~Gi")
    
    # create data frame for plot
    df <- rbind(yt.xtyi.xt.mean.std, yt.xtyi.yi.mean.std, prs.sub.mean.std, 
        yt.inter.mean.std)
    ratio <- max(1, nrow(yt.inter)/40)
    cat
    p <- ggplot(df) + geom_point(aes(x = SNP, y = Mean)) + geom_errorbar(aes(x = SNP, 
        ymin = Mean - 1.96 * Std, ymax = Mean + 1.96 * Std), 
        colour = "black", width = 0.1) + geom_hline(yintercept = 0, 
        color = "red") + facet_grid(. ~ Type, scales = "free_x") + 
        coord_flip() + theme(axis.text.x = element_text(angle = 90, 
        hjust = 1))
    p2 <- ggplot(yt.inter) + geom_bar(aes(x = SNP, y = -log10(P)), 
        stat = "identity") + coord_flip() + ggtitle("Interaction P-value")
    subchunkify(p, ratio)
    subchunkify(p2, ratio)
    cat("
")
    inter.plus.gwas.pval <- cbind(yt.inter, yt.xtyi.xt$P)
    colnames(inter.plus.gwas.pval) <- c(colnames(yt.inter), "GWAS.P")
    pander(inter.plus.gwas.pval[order(inter.plus.gwas.pval$P, 
        decreasing = F), ])
    cat("
")
    cat("
")
}

p1.0000e+00

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
114 12 rs2398486 0 T ADDxPRS 4864 1.685 2.114 0.03449 3.722e-05
117 12 rs2167512 0 A ADDxPRS 4864 1.717 2.112 0.03473 2.589e-05
9 1 rs2883720 0 T ADDxPRS 4864 0.7399 -1.969 0.04896 4.044e-05
126 16 rs7199903 0 T ADDxPRS 4864 0.8314 -1.249 0.2118 2.311e-05
81 9 rs564398 0 C ADDxPRS 4864 1.181 1.129 0.2589 7.542e-09
84 9 rs7865618 0 G ADDxPRS 4864 1.177 1.112 0.2659 1.155e-09
138 20 rs6071467 0 G ADDxPRS 4864 1.186 1.061 0.2885 4.436e-05
21 2 rs2943634 0 A ADDxPRS 4864 1.18 1.046 0.2956 1.381e-05
18 2 rs17018897 0 G ADDxPRS 4864 1.191 0.9229 0.356 2.845e-05
135 19 rs7250581 0 A ADDxPRS 4864 1.18 0.894 0.3713 9.666e-06
111 10 rs7910044 0 A ADDxPRS 4864 0.8844 -0.8397 0.4011 3.062e-05
150 22 rs688034 0 T ADDxPRS 4864 0.8822 -0.8155 0.4148 1.052e-05
3 1 rs10914783 0 A ADDxPRS 4864 1.319 0.7658 0.4438 3.562e-06
147 21 rs2838756 0 C ADDxPRS 4864 1.126 0.736 0.4617 2.911e-05
60 9 rs523096 0 G ADDxPRS 4864 1.108 0.6996 0.4842 1.209e-06
87 9 rs10965219 0 G ADDxPRS 4864 0.9077 -0.6681 0.504 6.55e-11
75 9 rs7049105 0 G ADDxPRS 4864 0.9106 -0.6462 0.5182 1.158e-09
48 6 rs6922269 0 A ADDxPRS 4864 0.9006 -0.644 0.5196 8.38e-06
105 9 rs1333048 0 A ADDxPRS 4864 1.089 0.5838 0.5593 7.505e-14
78 9 rs10965215 0 A ADDxPRS 4864 0.9204 -0.5733 0.5665 4.87e-10
30 4 rs11939435 0 G ADDxPRS 4864 0.8755 -0.5604 0.5752 3.313e-05
42 5 rs565928 0 T ADDxPRS 4864 0.9038 -0.5565 0.5779 6.691e-06
36 5 rs449650 0 T ADDxPRS 4864 0.9045 -0.5521 0.5809 6.331e-06
99 9 rs2891168 0 A ADDxPRS 4864 1.076 0.5057 0.6131 3.502e-13
96 9 rs4977574 0 A ADDxPRS 4864 1.073 0.4824 0.6296 3.956e-13
93 9 rs6475606 0 C ADDxPRS 4864 1.073 0.482 0.6298 3.858e-14
39 5 rs436495 0 A ADDxPRS 4864 0.9216 -0.4492 0.6533 8.509e-06
102 9 rs1333042 0 A ADDxPRS 4864 1.063 0.4176 0.6762 1.008e-12
123 16 rs12716963 0 G ADDxPRS 4864 1.077 0.4131 0.6795 2.203e-05
120 14 rs10431700 0 G ADDxPRS 4864 0.9427 -0.3941 0.6935 2.699e-05
54 8 rs16872634 0 C ADDxPRS 4864 1.065 0.3901 0.6965 5.49e-05
132 17 rs6502872 0 T ADDxPRS 4864 1.028 0.1878 0.8511 3.572e-05
15 1 rs17465637 0 T ADDxPRS 4864 1.022 0.1314 0.8955 1.246e-05
12 1 rs2133189 0 C ADDxPRS 4864 1.021 0.1271 0.8989 1.407e-05
66 9 rs10757264 0 G ADDxPRS 4864 0.9845 -0.107 0.9148 2.301e-07
141 20 rs6071469 0 C ADDxPRS 4864 0.9919 -0.0509 0.9594 4.151e-05
6 1 rs599839 0 G ADDxPRS 4864 1.007 0.0401 0.968 3.755e-05
144 20 rs2093154 0 T ADDxPRS 4864 0.9946 -0.03365 0.9732 4.201e-05

p3.0000e-01

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
114 12 rs2398486 0 T ADDxPRS 4864 1.731 2.28 0.02261 3.785e-05
117 12 rs2167512 0 A ADDxPRS 4864 1.75 2.241 0.02505 2.654e-05
9 1 rs2883720 0 T ADDxPRS 4864 0.745 -1.993 0.04629 3.946e-05
81 9 rs564398 0 C ADDxPRS 4864 1.216 1.378 0.1682 7.58e-09
135 19 rs7250581 0 A ADDxPRS 4864 1.277 1.359 0.1742 9.328e-06
84 9 rs7865618 0 G ADDxPRS 4864 1.207 1.338 0.181 1.181e-09
126 16 rs7199903 0 T ADDxPRS 4864 0.8287 -1.318 0.1874 2.288e-05
147 21 rs2838756 0 C ADDxPRS 4864 1.171 1.017 0.3089 2.923e-05
138 20 rs6071467 0 G ADDxPRS 4864 1.164 0.986 0.3241 4.336e-05
21 2 rs2943634 0 A ADDxPRS 4864 1.155 0.948 0.3431 1.402e-05
75 9 rs7049105 0 G ADDxPRS 4864 0.8767 -0.9444 0.3449 1.197e-09
18 2 rs17018897 0 G ADDxPRS 4864 1.185 0.9288 0.353 2.847e-05
60 9 rs523096 0 G ADDxPRS 4864 1.138 0.9205 0.3573 1.215e-06
87 9 rs10965219 0 G ADDxPRS 4864 0.8828 -0.895 0.3708 6.791e-11
78 9 rs10965215 0 A ADDxPRS 4864 0.8871 -0.8604 0.3895 5.07e-10
3 1 rs10914783 0 A ADDxPRS 4864 1.342 0.8476 0.3966 3.558e-06
30 4 rs11939435 0 G ADDxPRS 4864 0.8349 -0.7917 0.4285 3.461e-05
111 10 rs7910044 0 A ADDxPRS 4864 0.9007 -0.7421 0.458 3.107e-05
48 6 rs6922269 0 A ADDxPRS 4864 0.8943 -0.7149 0.4747 8.469e-06
93 9 rs6475606 0 C ADDxPRS 4864 1.09 0.6143 0.539 3.613e-14
42 5 rs565928 0 T ADDxPRS 4864 0.8989 -0.6119 0.5406 6.864e-06
36 5 rs449650 0 T ADDxPRS 4864 0.9021 -0.5917 0.5541 6.499e-06
105 9 rs1333048 0 A ADDxPRS 4864 1.083 0.5683 0.5699 7.105e-14
150 22 rs688034 0 T ADDxPRS 4864 0.921 -0.5563 0.578 1.038e-05
99 9 rs2891168 0 A ADDxPRS 4864 1.076 0.5221 0.6016 3.281e-13
39 5 rs436495 0 A ADDxPRS 4864 0.9156 -0.5066 0.6124 8.736e-06
96 9 rs4977574 0 A ADDxPRS 4864 1.073 0.5025 0.6153 3.709e-13
102 9 rs1333042 0 A ADDxPRS 4864 1.068 0.4706 0.6379 9.497e-13
123 16 rs12716963 0 G ADDxPRS 4864 1.082 0.4607 0.645 2.127e-05
54 8 rs16872634 0 C ADDxPRS 4864 1.067 0.4199 0.6746 5.635e-05
66 9 rs10757264 0 G ADDxPRS 4864 0.9553 -0.3251 0.7451 2.365e-07
120 14 rs10431700 0 G ADDxPRS 4864 0.9552 -0.3173 0.751 2.609e-05
6 1 rs599839 0 G ADDxPRS 4864 1.042 0.2406 0.8099 5.244e-05
15 1 rs17465637 0 T ADDxPRS 4864 1.019 0.1175 0.9064 1.247e-05
132 17 rs6502872 0 T ADDxPRS 4864 1.015 0.1089 0.9133 3.383e-05
141 20 rs6071469 0 C ADDxPRS 4864 0.9834 -0.1086 0.9135 4.047e-05
12 1 rs2133189 0 C ADDxPRS 4864 1.016 0.09959 0.9207 1.401e-05
144 20 rs2093154 0 T ADDxPRS 4864 0.986 -0.09117 0.9274 4.097e-05

p1.0000e-01

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
114 12 rs2398486 0 T ADDxPRS 4864 1.621 2.446 0.01444 3.921e-05
117 12 rs2167512 0 A ADDxPRS 4864 1.602 2.298 0.02158 2.805e-05
135 19 rs7250581 0 A ADDxPRS 4864 1.369 2.148 0.03168 8.762e-06
81 9 rs564398 0 C ADDxPRS 4864 1.237 1.872 0.06126 8.176e-09
9 1 rs2883720 0 T ADDxPRS 4864 0.801 -1.848 0.06463 3.802e-05
84 9 rs7865618 0 G ADDxPRS 4864 1.221 1.78 0.07509 1.319e-09
75 9 rs7049105 0 G ADDxPRS 4864 0.8354 -1.612 0.107 1.33e-09
147 21 rs2838756 0 C ADDxPRS 4864 1.213 1.545 0.1223 2.876e-05
78 9 rs10965215 0 A ADDxPRS 4864 0.844 -1.519 0.1288 5.716e-10
60 9 rs523096 0 G ADDxPRS 4864 1.174 1.423 0.1547 1.29e-06
126 16 rs7199903 0 T ADDxPRS 4864 0.851 -1.41 0.1585 2.05e-05
87 9 rs10965219 0 G ADDxPRS 4864 0.8567 -1.391 0.1642 7.711e-11
30 4 rs11939435 0 G ADDxPRS 4864 0.796 -1.254 0.2099 3.913e-05
93 9 rs6475606 0 C ADDxPRS 4864 1.115 0.9616 0.3362 3.642e-14
66 9 rs10757264 0 G ADDxPRS 4864 0.9067 -0.8658 0.3866 2.501e-07
3 1 rs10914783 0 A ADDxPRS 4864 1.258 0.8577 0.391 3.557e-06
18 2 rs17018897 0 G ADDxPRS 4864 1.129 0.8216 0.4113 2.949e-05
48 6 rs6922269 0 A ADDxPRS 4864 0.9087 -0.7639 0.4449 8.299e-06
138 20 rs6071467 0 G ADDxPRS 4864 1.089 0.6905 0.4899 3.979e-05
6 1 rs599839 0 G ADDxPRS 4864 1.097 0.6723 0.5014 0.0001037
42 5 rs565928 0 T ADDxPRS 4864 0.9133 -0.654 0.5131 7.374e-06
102 9 rs1333042 0 A ADDxPRS 4864 1.076 0.6518 0.5145 9.712e-13
99 9 rs2891168 0 A ADDxPRS 4864 1.073 0.6225 0.5336 3.349e-13
96 9 rs4977574 0 A ADDxPRS 4864 1.071 0.6134 0.5396 3.797e-13
36 5 rs449650 0 T ADDxPRS 4864 0.9199 -0.6013 0.5476 6.979e-06
105 9 rs1333048 0 A ADDxPRS 4864 1.069 0.5969 0.5505 7.323e-14
21 2 rs2943634 0 A ADDxPRS 4864 1.074 0.5829 0.56 1.369e-05
39 5 rs436495 0 A ADDxPRS 4864 0.9254 -0.56 0.5755 9.438e-06
123 16 rs12716963 0 G ADDxPRS 4864 1.073 0.5127 0.6082 2.238e-05
54 8 rs16872634 0 C ADDxPRS 4864 1.064 0.4988 0.6179 5.716e-05
111 10 rs7910044 0 A ADDxPRS 4864 0.9571 -0.3861 0.6994 3.399e-05
141 20 rs6071469 0 C ADDxPRS 4864 0.9731 -0.2206 0.8254 3.597e-05
144 20 rs2093154 0 T ADDxPRS 4864 0.9751 -0.2043 0.8381 3.644e-05
132 17 rs6502872 0 T ADDxPRS 4864 0.9871 -0.1147 0.9086 3.226e-05
150 22 rs688034 0 T ADDxPRS 4864 1.011 0.09525 0.9241 1.011e-05
120 14 rs10431700 0 G ADDxPRS 4864 0.9914 -0.0739 0.9411 2.453e-05
12 1 rs2133189 0 C ADDxPRS 4864 0.9952 -0.03792 0.9698 1.352e-05
15 1 rs17465637 0 T ADDxPRS 4864 1.002 0.0174 0.9861 1.224e-05

p3.0000e-02

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
135 19 rs7250581 0 A ADDxPRS 4864 1.237 2.395 0.01664 8.756e-06
114 12 rs2398486 0 T ADDxPRS 4864 1.31 2.232 0.02561 3.841e-05
81 9 rs564398 0 C ADDxPRS 4864 1.161 2.147 0.03183 9.123e-09
84 9 rs7865618 0 G ADDxPRS 4864 1.151 2.041 0.04126 1.476e-09
75 9 rs7049105 0 G ADDxPRS 4864 0.8724 -2 0.04552 1.426e-09
117 12 rs2167512 0 A ADDxPRS 4864 1.285 1.987 0.04688 2.798e-05
78 9 rs10965215 0 A ADDxPRS 4864 0.8768 -1.926 0.05413 6.17e-10
147 21 rs2838756 0 C ADDxPRS 4864 1.158 1.924 0.05438 2.743e-05
60 9 rs523096 0 G ADDxPRS 4864 1.134 1.818 0.06899 1.382e-06
87 9 rs10965219 0 G ADDxPRS 4864 0.8938 -1.656 0.09781 8.495e-11
30 4 rs11939435 0 G ADDxPRS 4864 0.8391 -1.57 0.1164 4.234e-05
9 1 rs2883720 0 T ADDxPRS 4864 0.8987 -1.436 0.1511 3.86e-05
126 16 rs7199903 0 T ADDxPRS 4864 0.908 -1.382 0.1671 1.725e-05
93 9 rs6475606 0 C ADDxPRS 4864 1.09 1.252 0.2104 4.478e-14
66 9 rs10757264 0 G ADDxPRS 4864 0.9236 -1.147 0.2513 2.468e-07
6 1 rs599839 0 G ADDxPRS 4864 1.08 0.9164 0.3595 0.0001502
102 9 rs1333042 0 A ADDxPRS 4864 1.055 0.78 0.4354 1.206e-12
48 6 rs6922269 0 A ADDxPRS 4864 0.942 -0.7756 0.438 7.7e-06
3 1 rs10914783 0 A ADDxPRS 4864 1.122 0.7394 0.4597 3.583e-06
96 9 rs4977574 0 A ADDxPRS 4864 1.051 0.7151 0.4746 4.791e-13
99 9 rs2891168 0 A ADDxPRS 4864 1.05 0.7122 0.4763 4.208e-13
150 22 rs688034 0 T ADDxPRS 4864 1.051 0.6822 0.4951 1.017e-05
105 9 rs1333048 0 A ADDxPRS 4864 1.042 0.6022 0.547 9.119e-14
42 5 rs565928 0 T ADDxPRS 4864 0.9527 -0.5743 0.5657 8.124e-06
18 2 rs17018897 0 G ADDxPRS 4864 1.048 0.5272 0.598 3.238e-05
54 8 rs16872634 0 C ADDxPRS 4864 1.04 0.5071 0.6121 5.5e-05
39 5 rs436495 0 A ADDxPRS 4864 0.9585 -0.5014 0.6161 1.051e-05
36 5 rs449650 0 T ADDxPRS 4864 0.9589 -0.4956 0.6202 7.666e-06
123 16 rs12716963 0 G ADDxPRS 4864 1.039 0.4521 0.6512 2.766e-05
132 17 rs6502872 0 T ADDxPRS 4864 0.9701 -0.433 0.665 3.505e-05
12 1 rs2133189 0 C ADDxPRS 4864 0.9754 -0.3204 0.7486 1.278e-05
138 20 rs6071467 0 G ADDxPRS 4864 1.02 0.2611 0.794 3.575e-05
15 1 rs17465637 0 T ADDxPRS 4864 0.9807 -0.25 0.8026 1.171e-05
141 20 rs6071469 0 C ADDxPRS 4864 0.9849 -0.2019 0.84 3.027e-05
144 20 rs2093154 0 T ADDxPRS 4864 0.9859 -0.1892 0.8499 3.064e-05
111 10 rs7910044 0 A ADDxPRS 4864 1.008 0.1124 0.9105 3.905e-05
21 2 rs2943634 0 A ADDxPRS 4864 1.003 0.04107 0.9672 1.199e-05
120 14 rs10431700 0 G ADDxPRS 4864 1.002 0.03291 0.9737 2.422e-05

p1.0000e-02

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
135 19 rs7250581 0 A ADDxPRS 4864 1.151 2.257 0.02398 8.889e-06
81 9 rs564398 0 C ADDxPRS 4864 1.111 2.121 0.03393 9.505e-09
147 21 rs2838756 0 C ADDxPRS 4864 1.119 2.084 0.03714 2.71e-05
75 9 rs7049105 0 G ADDxPRS 4864 0.9067 -2.024 0.04298 1.436e-09
84 9 rs7865618 0 G ADDxPRS 4864 1.104 2.013 0.04413 1.521e-09
78 9 rs10965215 0 A ADDxPRS 4864 0.9099 -1.953 0.05086 6.192e-10
60 9 rs523096 0 G ADDxPRS 4864 1.098 1.896 0.058 1.407e-06
114 12 rs2398486 0 T ADDxPRS 4864 1.175 1.885 0.05937 3.757e-05
30 4 rs11939435 0 G ADDxPRS 4864 0.8762 -1.661 0.0968 4.22e-05
87 9 rs10965219 0 G ADDxPRS 4864 0.9255 -1.609 0.1076 8.631e-11
117 12 rs2167512 0 A ADDxPRS 4864 1.152 1.584 0.1133 2.747e-05
126 16 rs7199903 0 T ADDxPRS 4864 0.9362 -1.334 0.1822 1.593e-05
93 9 rs6475606 0 C ADDxPRS 4864 1.064 1.274 0.2027 5.113e-14
66 9 rs10757264 0 G ADDxPRS 4864 0.9447 -1.157 0.2474 2.378e-07
9 1 rs2883720 0 T ADDxPRS 4864 0.9426 -1.114 0.2652 3.91e-05
6 1 rs599839 0 G ADDxPRS 4864 1.06 0.9693 0.3324 0.0001427
150 22 rs688034 0 T ADDxPRS 4864 1.051 0.9663 0.3339 1.027e-05
48 6 rs6922269 0 A ADDxPRS 4864 0.9543 -0.8516 0.3944 7.275e-06
102 9 rs1333042 0 A ADDxPRS 4864 1.039 0.7728 0.4396 1.376e-12
96 9 rs4977574 0 A ADDxPRS 4864 1.035 0.6974 0.4855 5.521e-13
99 9 rs2891168 0 A ADDxPRS 4864 1.034 0.6876 0.4917 4.839e-13
3 1 rs10914783 0 A ADDxPRS 4864 1.073 0.6435 0.5199 3.624e-06
132 17 rs6502872 0 T ADDxPRS 4864 0.9726 -0.5555 0.5786 3.812e-05
105 9 rs1333048 0 A ADDxPRS 4864 1.027 0.5343 0.5931 1.039e-13
12 1 rs2133189 0 C ADDxPRS 4864 0.9745 -0.4674 0.6402 1.225e-05
42 5 rs565928 0 T ADDxPRS 4864 0.9735 -0.4477 0.6544 8.301e-06
123 16 rs12716963 0 G ADDxPRS 4864 1.027 0.444 0.6571 3.204e-05
54 8 rs16872634 0 C ADDxPRS 4864 1.022 0.4025 0.6873 5.296e-05
15 1 rs17465637 0 T ADDxPRS 4864 0.9782 -0.3993 0.6897 1.126e-05
39 5 rs436495 0 A ADDxPRS 4864 0.9768 -0.3903 0.6963 1.078e-05
21 2 rs2943634 0 A ADDxPRS 4864 0.9809 -0.3676 0.7132 1.105e-05
36 5 rs449650 0 T ADDxPRS 4864 0.9784 -0.3621 0.7173 7.796e-06
111 10 rs7910044 0 A ADDxPRS 4864 1.017 0.3423 0.7321 4.098e-05
18 2 rs17018897 0 G ADDxPRS 4864 1.016 0.2445 0.8068 3.426e-05
120 14 rs10431700 0 G ADDxPRS 4864 1.008 0.1523 0.8789 2.427e-05
141 20 rs6071469 0 C ADDxPRS 4864 0.9941 -0.111 0.9117 2.872e-05
144 20 rs2093154 0 T ADDxPRS 4864 0.9947 -0.09984 0.9205 2.906e-05
138 20 rs6071467 0 G ADDxPRS 4864 1.002 0.04658 0.9628 3.47e-05

p3.0000e-03

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
135 19 rs7250581 0 A ADDxPRS 4864 1.128 2.175 0.0296 9.01e-06
147 21 rs2838756 0 C ADDxPRS 4864 1.11 2.167 0.03023 2.677e-05
75 9 rs7049105 0 G ADDxPRS 4864 0.911 -2.163 0.03053 1.441e-09
78 9 rs10965215 0 A ADDxPRS 4864 0.9141 -2.084 0.03715 6.183e-10
81 9 rs564398 0 C ADDxPRS 4864 1.093 2.007 0.04476 9.801e-09
84 9 rs7865618 0 G ADDxPRS 4864 1.086 1.879 0.06027 1.58e-09
60 9 rs523096 0 G ADDxPRS 4864 1.086 1.867 0.06196 1.442e-06
87 9 rs10965219 0 G ADDxPRS 4864 0.9304 -1.681 0.09281 8.709e-11
30 4 rs11939435 0 G ADDxPRS 4864 0.888 -1.673 0.09436 4.121e-05
114 12 rs2398486 0 T ADDxPRS 4864 1.13 1.617 0.1059 3.794e-05
66 9 rs10757264 0 G ADDxPRS 4864 0.9405 -1.4 0.1615 2.356e-07
117 12 rs2167512 0 A ADDxPRS 4864 1.105 1.267 0.2051 2.74e-05
93 9 rs6475606 0 C ADDxPRS 4864 1.054 1.207 0.2273 5.505e-14
150 22 rs688034 0 T ADDxPRS 4864 1.052 1.105 0.2692 1.038e-05
126 16 rs7199903 0 T ADDxPRS 4864 0.9555 -1.032 0.3022 1.537e-05
6 1 rs599839 0 G ADDxPRS 4864 1.053 0.9654 0.3343 0.0001275
48 6 rs6922269 0 A ADDxPRS 4864 0.9618 -0.7923 0.4282 7.08e-06
102 9 rs1333042 0 A ADDxPRS 4864 1.034 0.7681 0.4424 1.473e-12
9 1 rs2883720 0 T ADDxPRS 4864 0.9655 -0.7368 0.4612 4.013e-05
132 17 rs6502872 0 T ADDxPRS 4864 0.9694 -0.697 0.4858 4.077e-05
96 9 rs4977574 0 A ADDxPRS 4864 1.028 0.6275 0.5303 6.027e-13
99 9 rs2891168 0 A ADDxPRS 4864 1.027 0.6132 0.5398 5.278e-13
21 2 rs2943634 0 A ADDxPRS 4864 0.9737 -0.5677 0.5702 1.116e-05
111 10 rs7910044 0 A ADDxPRS 4864 1.025 0.5523 0.5807 4.123e-05
12 1 rs2133189 0 C ADDxPRS 4864 0.9782 -0.447 0.6549 1.205e-05
42 5 rs565928 0 T ADDxPRS 4864 0.9768 -0.4379 0.6614 7.977e-06
123 16 rs12716963 0 G ADDxPRS 4864 1.024 0.4366 0.6624 3.46e-05
105 9 rs1333048 0 A ADDxPRS 4864 1.019 0.4318 0.6659 1.122e-13
3 1 rs10914783 0 A ADDxPRS 4864 1.04 0.4062 0.6846 3.692e-06
39 5 rs436495 0 A ADDxPRS 4864 0.9791 -0.3928 0.6945 1.036e-05
15 1 rs17465637 0 T ADDxPRS 4864 0.9817 -0.3758 0.707 1.11e-05
120 14 rs10431700 0 G ADDxPRS 4864 1.016 0.3632 0.7165 2.433e-05
36 5 rs449650 0 T ADDxPRS 4864 0.9809 -0.3586 0.7199 7.448e-06
54 8 rs16872634 0 C ADDxPRS 4864 1.012 0.2535 0.7999 5.296e-05
138 20 rs6071467 0 G ADDxPRS 4864 0.9938 -0.1325 0.8946 3.532e-05
141 20 rs6071469 0 C ADDxPRS 4864 0.9943 -0.1188 0.9055 2.965e-05
144 20 rs2093154 0 T ADDxPRS 4864 0.9947 -0.1112 0.9114 2.996e-05
18 2 rs17018897 0 G ADDxPRS 4864 0.9979 -0.03811 0.9696 3.513e-05

p1.0000e-03

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
75 9 rs7049105 0 G ADDxPRS 4864 0.9051 -2.272 0.02308 1.465e-09
78 9 rs10965215 0 A ADDxPRS 4864 0.9088 -2.183 0.02905 6.302e-10
147 21 rs2838756 0 C ADDxPRS 4864 1.109 2.119 0.03409 2.577e-05
135 19 rs7250581 0 A ADDxPRS 4864 1.124 2.09 0.03666 9.135e-06
81 9 rs564398 0 C ADDxPRS 4864 1.087 1.867 0.06185 1.02e-08
60 9 rs523096 0 G ADDxPRS 4864 1.082 1.751 0.08002 1.506e-06
87 9 rs10965219 0 G ADDxPRS 4864 0.9264 -1.748 0.08041 8.948e-11
84 9 rs7865618 0 G ADDxPRS 4864 1.079 1.709 0.08741 1.666e-09
66 9 rs10757264 0 G ADDxPRS 4864 0.928 -1.674 0.09415 2.398e-07
30 4 rs11939435 0 G ADDxPRS 4864 0.8908 -1.604 0.1087 4.084e-05
114 12 rs2398486 0 T ADDxPRS 4864 1.114 1.421 0.1553 3.926e-05
150 22 rs688034 0 T ADDxPRS 4864 1.059 1.213 0.225 1.054e-05
117 12 rs2167512 0 A ADDxPRS 4864 1.09 1.08 0.2804 2.794e-05
93 9 rs6475606 0 C ADDxPRS 4864 1.049 1.076 0.2817 5.715e-14
6 1 rs599839 0 G ADDxPRS 4864 1.056 0.9948 0.3198 0.0001296
132 17 rs6502872 0 T ADDxPRS 4864 0.9645 -0.7956 0.4263 4.13e-05
126 16 rs7199903 0 T ADDxPRS 4864 0.9681 -0.7204 0.4713 1.509e-05
102 9 rs1333042 0 A ADDxPRS 4864 1.032 0.713 0.4759 1.534e-12
111 10 rs7910044 0 A ADDxPRS 4864 1.03 0.665 0.5061 4.11e-05
48 6 rs6922269 0 A ADDxPRS 4864 0.9673 -0.6646 0.5063 6.971e-06
9 1 rs2883720 0 T ADDxPRS 4864 0.9734 -0.5546 0.5791 4.053e-05
21 2 rs2943634 0 A ADDxPRS 4864 0.9743 -0.5447 0.586 1.164e-05
96 9 rs4977574 0 A ADDxPRS 4864 1.024 0.5254 0.5993 6.414e-13
99 9 rs2891168 0 A ADDxPRS 4864 1.023 0.5071 0.6121 5.611e-13
42 5 rs565928 0 T ADDxPRS 4864 0.973 -0.5016 0.616 7.624e-06
39 5 rs436495 0 A ADDxPRS 4864 0.9751 -0.4612 0.6446 9.9e-06
123 16 rs12716963 0 G ADDxPRS 4864 1.025 0.4454 0.656 3.569e-05
36 5 rs449650 0 T ADDxPRS 4864 0.9767 -0.4287 0.6681 7.088e-06
120 14 rs10431700 0 G ADDxPRS 4864 1.018 0.3949 0.6929 2.474e-05
12 1 rs2133189 0 C ADDxPRS 4864 0.9817 -0.3677 0.7131 1.191e-05
105 9 rs1333048 0 A ADDxPRS 4864 1.015 0.3236 0.7462 1.192e-13
15 1 rs17465637 0 T ADDxPRS 4864 0.986 -0.2797 0.7797 1.098e-05
3 1 rs10914783 0 A ADDxPRS 4864 1.016 0.16 0.8729 3.696e-06
138 20 rs6071467 0 G ADDxPRS 4864 0.9932 -0.1442 0.8854 3.598e-05
54 8 rs16872634 0 C ADDxPRS 4864 1.007 0.1401 0.8886 5.444e-05
141 20 rs6071469 0 C ADDxPRS 4864 0.9937 -0.1303 0.8963 3.072e-05
144 20 rs2093154 0 T ADDxPRS 4864 0.994 -0.1246 0.9009 3.104e-05
18 2 rs17018897 0 G ADDxPRS 4864 0.9931 -0.1213 0.9035 3.422e-05

p3.0000e-04

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
75 9 rs7049105 0 G ADDxPRS 4864 0.8991 -2.329 0.01986 1.504e-09
135 19 rs7250581 0 A ADDxPRS 4864 1.138 2.238 0.02519 9.215e-06
78 9 rs10965215 0 A ADDxPRS 4864 0.9037 -2.22 0.02643 6.496e-10
147 21 rs2838756 0 C ADDxPRS 4864 1.105 1.992 0.04635 2.523e-05
66 9 rs10757264 0 G ADDxPRS 4864 0.9169 -1.866 0.06208 2.462e-07
87 9 rs10965219 0 G ADDxPRS 4864 0.9219 -1.785 0.07418 9.318e-11
81 9 rs564398 0 C ADDxPRS 4864 1.086 1.769 0.07691 1.083e-08
60 9 rs523096 0 G ADDxPRS 4864 1.078 1.608 0.1079 1.611e-06
84 9 rs7865618 0 G ADDxPRS 4864 1.076 1.571 0.1162 1.789e-09
30 4 rs11939435 0 G ADDxPRS 4864 0.8988 -1.431 0.1525 4.091e-05
114 12 rs2398486 0 T ADDxPRS 4864 1.112 1.354 0.1757 4.103e-05
150 22 rs688034 0 T ADDxPRS 4864 1.067 1.314 0.1888 1.065e-05
6 1 rs599839 0 G ADDxPRS 4864 1.064 1.077 0.2814 0.0001366
117 12 rs2167512 0 A ADDxPRS 4864 1.089 1.04 0.2982 2.895e-05
93 9 rs6475606 0 C ADDxPRS 4864 1.045 0.9537 0.3402 6.087e-14
132 17 rs6502872 0 T ADDxPRS 4864 0.9649 -0.7587 0.448 4.027e-05
111 10 rs7910044 0 A ADDxPRS 4864 1.032 0.664 0.5067 4.121e-05
102 9 rs1333042 0 A ADDxPRS 4864 1.031 0.6593 0.5097 1.628e-12
9 1 rs2883720 0 T ADDxPRS 4864 0.9705 -0.5952 0.5517 4.058e-05
123 16 rs12716963 0 G ADDxPRS 4864 1.034 0.5751 0.5652 3.601e-05
126 16 rs7199903 0 T ADDxPRS 4864 0.975 -0.5428 0.5872 1.52e-05
48 6 rs6922269 0 A ADDxPRS 4864 0.9751 -0.4858 0.6271 7.005e-06
96 9 rs4977574 0 A ADDxPRS 4864 1.02 0.4335 0.6646 6.925e-13
42 5 rs565928 0 T ADDxPRS 4864 0.9757 -0.4311 0.6664 7.427e-06
21 2 rs2943634 0 A ADDxPRS 4864 0.9798 -0.4111 0.681 1.253e-05
99 9 rs2891168 0 A ADDxPRS 4864 1.019 0.4106 0.6814 6.05e-13
120 14 rs10431700 0 G ADDxPRS 4864 1.019 0.3985 0.6903 2.556e-05
39 5 rs436495 0 A ADDxPRS 4864 0.9779 -0.391 0.6958 9.63e-06
36 5 rs449650 0 T ADDxPRS 4864 0.9808 -0.3379 0.7354 6.913e-06
105 9 rs1333048 0 A ADDxPRS 4864 1.011 0.2343 0.8148 1.278e-13
141 20 rs6071469 0 C ADDxPRS 4864 0.989 -0.2192 0.8265 3.131e-05
144 20 rs2093154 0 T ADDxPRS 4864 0.9893 -0.214 0.8306 3.163e-05
18 2 rs17018897 0 G ADDxPRS 4864 0.9902 -0.1666 0.8677 3.285e-05
12 1 rs2133189 0 C ADDxPRS 4864 0.9914 -0.1649 0.869 1.198e-05
138 20 rs6071467 0 G ADDxPRS 4864 0.9929 -0.1442 0.8854 3.629e-05
54 8 rs16872634 0 C ADDxPRS 4864 1.007 0.1291 0.8973 5.434e-05
15 1 rs17465637 0 T ADDxPRS 4864 0.9972 -0.05453 0.9565 1.104e-05
3 1 rs10914783 0 A ADDxPRS 4864 1.003 0.03033 0.9758 3.708e-06

p1.0000e-04

  CHR SNP BP A1 TEST NMISS OR STAT P GWAS.P
75 9 rs7049105 0 G ADDxPRS 4864 0.8961 -2.326 0.02002 1.543e-09
135 19 rs7250581 0 A ADDxPRS 4864 1.147 2.305 0.02115 9.491e-06
78 9 rs10965215 0 A ADDxPRS 4864 0.9016 -2.196 0.02807 6.677e-10
66 9 rs10757264 0 G ADDxPRS 4864 0.9121 -1.914 0.0556 2.539e-07
147 21 rs2838756 0 C ADDxPRS 4864 1.103 1.897 0.05777 2.527e-05
87 9 rs10965219 0 G ADDxPRS 4864 0.9204 -1.762 0.07803 9.632e-11
81 9 rs564398 0 C ADDxPRS 4864 1.086 1.72 0.08536 1.125e-08
60 9 rs523096 0 G ADDxPRS 4864 1.076 1.517 0.1294 1.69e-06
84 9 rs7865618 0 G ADDxPRS 4864 1.074 1.495 0.1349 1.864e-09
150 22 rs688034 0 T ADDxPRS 4864 1.076 1.438 0.1504 1.082e-05
30 4 rs11939435 0 G ADDxPRS 4864 0.9024 -1.341 0.1798 4.063e-05
114 12 rs2398486 0 T ADDxPRS 4864 1.11 1.3 0.1936 4.207e-05
6 1 rs599839 0 G ADDxPRS 4864 1.066 1.077 0.2814 0.0001411
117 12 rs2167512 0 A ADDxPRS 4864 1.088 1.005 0.3148 2.953e-05
93 9 rs6475606 0 C ADDxPRS 4864 1.041 0.8406 0.4006 6.332e-14
9 1 rs2883720 0 T ADDxPRS 4864 0.965 -0.6866 0.4923 4.033e-05
123 16 rs12716963 0 G ADDxPRS 4864 1.042 0.6861 0.4927 3.637e-05
132 17 rs6502872 0 T ADDxPRS 4864 0.9699 -0.6305 0.5284 3.944e-05
111 10 rs7910044 0 A ADDxPRS 4864 1.03 0.6136 0.5395 4.085e-05
102 9 rs1333042 0 A ADDxPRS 4864 1.029 0.592 0.5538 1.691e-12
126 16 rs7199903 0 T ADDxPRS 4864 0.9747 -0.533 0.594 1.535e-05
120 14 rs10431700 0 G ADDxPRS 4864 1.022 0.4543 0.6496 2.584e-05
48 6 rs6922269 0 A ADDxPRS 4864 0.979 -0.3968 0.6915 6.981e-06
42 5 rs565928 0 T ADDxPRS 4864 0.9786 -0.3666 0.7139 7.312e-06
96 9 rs4977574 0 A ADDxPRS 4864 1.017 0.3516 0.7251 7.177e-13
39 5 rs436495 0 A ADDxPRS 4864 0.9806 -0.3306 0.741 9.472e-06
99 9 rs2891168 0 A ADDxPRS 4864 1.016 0.3251 0.7451 6.264e-13
21 2 rs2943634 0 A ADDxPRS 4864 0.9841 -0.3146 0.753 1.312e-05
36 5 rs449650 0 T ADDxPRS 4864 0.9847 -0.2603 0.7947 6.819e-06
141 20 rs6071469 0 C ADDxPRS 4864 0.9871 -0.2509 0.8019 3.167e-05
144 20 rs2093154 0 T ADDxPRS 4864 0.9874 -0.2447 0.8067 3.2e-05
18 2 rs17018897 0 G ADDxPRS 4864 0.9888 -0.1842 0.8539 3.189e-05
105 9 rs1333048 0 A ADDxPRS 4864 1.008 0.1617 0.8716 1.317e-13
138 20 rs6071467 0 G ADDxPRS 4864 0.994 -0.1187 0.9055 3.66e-05
54 8 rs16872634 0 C ADDxPRS 4864 1.004 0.08365 0.9333 5.402e-05
12 1 rs2133189 0 C ADDxPRS 4864 0.9965 -0.06473 0.9484 1.194e-05
15 1 rs17465637 0 T ADDxPRS 4864 1.003 0.05859 0.9533 1.099e-05
3 1 rs10914783 0 A ADDxPRS 4864 0.9954 -0.04511 0.964 3.709e-06